(1) Ideally I would like for the circle to show up in a ray-traced rendering, so a torus would probably be better than a line drawing. Currently it is only useful for interactive display. In the attached example, I am using colored circles and text to label atoms that have formal charge in a reactive MD simulation. (My script redraws the circle when there is a change in the viewing angle, so it is always in the plane of the image and looks like a circle.)

(2) I'm mainly hoping to get the five platonic solids, because it's cool to draw them as graphics in order to label things. Of course there are lots of cool 3D shapes out there but I think these would be great starting points.

(3) I think this would be awesome. One of the ways I use VMD is to visualize a reaction network where collections of compounds undergo transformations, and if I could mouse-over a reaction node, then I could have it display an image with the reaction barrier.

Hi,
I have a few short questions for you that will help me answer
your questions in the best way possible.

1) For the "circles" you want to draw, are they merely meant for
interactive display, as line-drawn circles, or would you prefer
something that would also show up in a ray traced rendering of
the scene (e.g. Tachyon, POV-Ray, etc), in which case you'd really
want a torus and not a circle.

2) What polyhedra are you really after? Are there specific shapes you want?
Modern OpenGL has moved away from rendering methods that are based on
immediate mode commands, and even display lists. Small polyhedra fall into
a gray area between what could be done efficiently with OpenGL 1.x and
the minimum geometry size that can be drawn with reasonable performance on
modern hardware oriented towards OpenGL 3.x and 4.x. If you can tell me
more about what you're doing, I can give a useful answer as to whether it
is worth building in primitives for this in VMD or not.

3) There isn't a built-in way to do tooltips, and this would be problematic
for large structures with millions of atoms, but there is a way that a
user-written script can get callbacks as the mouse moves, and building
upon this, one could do a tooltip style interface if the number of potential
targets was moderate, and not all atoms.. :-)
I will have to dig up the code for this, as it has been some time since
I last looked at it, but there should be a way to do what you want using
the VMD mouse event callbacks and a little post-processing of the
returned coordinates, etc.